nucleR: a package for non-parametric nucleosome positioning

被引：74

作者：

Flores, Oscar ^{[1
]}

Orozco, Modesto ^{[1
,2
,3
]}

机构：

[1] IRB BSC Joint Res Program Computat Biol, Inst Res Biomed, Barcelona 08028, Spain

[2] Univ Barcelona, Dept Biochem & Mol Biol, E-08028 Barcelona, Spain

[3] Inst Nacl Bioinformat, Barcelona 08028, Spain

来源：

BIOINFORMATICS | 2011年 / 27卷 / 15期

关键词：

D O I：

10.1093/bioinformatics/btr345

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

nucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

引用

页码：2149 / 2150

页数：2

共 8 条

[1] A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data [J].

Chen, Xiaoyu ;

Hoffman, Michael M. ;

Bilmes, Jeff A. ;

Hesselberth, Jay R. ;

Noble, William S. .

BIOINFORMATICS, 2010, 26 (12) :i334-i342

[2]

DENIZ O, 2011, PHYS PROPER IN PRESS

[3] A multi-layer method to study genome-scale positions of nucleosomes [J].

Di Gesu, Vito ;

Lo Bosco, Giosue ;

Pinello, Luca ;

Yuan, Guo-Cheng ;

Corona, Davide F. V. .

GENOMICS, 2009, 93 (02) :140-145

[4] Nucleosome positioning and gene regulation: advances through genomics [J].

Jiang, Cizhong ;

Pugh, B. Franklin .

NATURE REVIEWS GENETICS, 2009, 10 (03) :161-172

[5] A high- resolution atlas of nucleosome occupancy in yeast [J].

Lee, William ;

Tillo, Desiree ;

Bray, Nicolas ;

Morse, Randall H. ;

Davis, Ronald W. ;

Hughes, Timothy R. ;

Nislow, Corey .

NATURE GENETICS, 2007, 39 (10) :1235-1244

[6]

Smith S.W., 1999, The Scientist and Engineer's Guide to Digital Signal Processing

[7] Nucleosome positioning from tiling microarray data [J].

Yassour, Moran ;

Kaplan, Tommy ;

Jaimovich, Ariel ;

Friedman, Nir .

BIOINFORMATICS, 2008, 24 (13) :I139-I146

[8] Genome-scale identification of nucleosome positions in S-cerevisiae [J].

Yuan, GC ;

Liu, YJ ;

Dion, MF ;

Slack, MD ;

Wu, LF ;

Altschuler, SJ ;

Rando, OJ .

SCIENCE, 2005, 309 (5734) :626-630

← 1 →